From 1f56ac6a4ae8e25499880177f34b4667ce0d6984 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Mon, 27 May 2019 19:14:09 -0600 Subject: [PATCH] streamlining and bugfixing of geom-class --- processing/pre/geom_addPrimitive.py | 30 +-- processing/pre/geom_canvas.py | 107 ++++++--- processing/pre/geom_clean.py | 8 +- processing/pre/geom_fromMinimalSurface.py | 7 +- processing/pre/geom_fromTable.py | 3 +- .../pre/geom_fromVoronoiTessellation.py | 3 +- processing/pre/geom_grainGrowth.py | 9 +- processing/pre/geom_mirror.py | 10 +- processing/pre/geom_pack.py | 42 ++-- processing/pre/geom_renumber.py | 8 +- processing/pre/geom_rescale.py | 38 ++- processing/pre/geom_rotate.py | 33 ++- processing/pre/geom_toTable.py | 13 +- processing/pre/geom_translate.py | 28 +-- processing/pre/geom_unpack.py | 8 +- processing/pre/geom_vicinityOffset.py | 14 +- python/damask/geom.py | 227 +++++++++--------- python/damask/util.py | 5 + test.log | 211 ++++++++++++++++ 19 files changed, 495 insertions(+), 309 deletions(-) create mode 100644 test.log diff --git a/processing/pre/geom_addPrimitive.py b/processing/pre/geom_addPrimitive.py index 65f13a2da..632019118 100755 --- a/processing/pre/geom_addPrimitive.py +++ b/processing/pre/geom_addPrimitive.py @@ -78,7 +78,7 @@ parser.set_defaults(center = (.0,.0,.0), if options.dimension is None: parser.error('no dimension specified.') -if [options.angleaxis,options.quaternion].count(None) == 2: +if [options.angleaxis,options.quaternion].count(None) == 0: parser.error('more than one rotation specified.') if options.angleaxis is not None: @@ -99,27 +99,18 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) + grid = geom.get_grid() + size = geom.get_size() + origin = geom.get_origin() microstructure = geom.get_microstructure() - fill = options.fill if options.fill is not None else np.nanmax(microstructure)+1 - - origin = np.zeros(3) - for i,line in enumerate(geom.comments): - if line.lower().strip().startswith('origin'): - origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z) - - # coordinates given in real space (default) vs voxel space + # coordinates given in real space, not (default) voxel space if options.realspace: options.center -= origin - options.center *= geom.get_grid() / geom.get_size() - options.dimension *= geom.get_grid() / geom.get_size() - - grid = microstructure.shape + options.center *= grid / size + options.dimension *= grid / size + # change to coordinate space where the primitive is the unit sphere/cube/etc if options.periodic: # use padding to achieve periodicity @@ -158,6 +149,7 @@ for name in filenames: Y /= options.dimension[1] * 0.5 Z /= options.dimension[2] * 0.5 + fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill # High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine old_settings = np.seterr() @@ -191,7 +183,7 @@ for name in filenames: microstructure if options.inside else fill) damask.util.croak(geom.update(microstructure)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_canvas.py b/processing/pre/geom_canvas.py index 0951ab1a5..3b7071968 100755 --- a/processing/pre/geom_canvas.py +++ b/processing/pre/geom_canvas.py @@ -1,80 +1,111 @@ #!/usr/bin/env python3 +# -*- coding: UTF-8 no BOM -*- import os import sys +import numpy as np +import damask + from io import StringIO from optparse import OptionParser -import numpy as np - -import damask - scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) - # -------------------------------------------------------------------- # MAIN # -------------------------------------------------------------------- -parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """ -Increases or decreases the (three-dimensional) canvas. +parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """ +Changes the (three-dimensional) canvas of a spectral geometry description. Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32. """, version = scriptID) -parser.add_option('-g','--grid', +parser.add_option('-g', + '--grid', dest = 'grid', type = 'string', nargs = 3, metavar = ' '.join(['string']*3), - help = 'a,b,c grid of hexahedral box') -parser.add_option('-o','--offset', + help = 'a,b,c grid of hexahedral box. [auto]') +parser.add_option('-o', + '--offset', dest = 'offset', type = 'int', nargs = 3, metavar = ' '.join(['int']*3), help = 'a,b,c offset from old to new origin of grid [%default]') -parser.add_option('-f','--fill', +parser.add_option('-f', + '--fill', dest = 'fill', - type = 'float', metavar = 'int', - help = 'background microstructure index, defaults to max microstructure index + 1') + type = 'float', metavar = 'float', + help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]') +parser.add_option('--blank', + dest = 'blank', + action = 'store_true', + help = 'blank out (optional) input canvas content') -parser.set_defaults(offset = (0,0,0)) +parser.set_defaults(grid = ['0','0','0'], + offset = (0,0,0), + ) (options, filenames) = parser.parse_args() +options.grid = ['1','1','1'] if options.blank and options.grid == ['0','0','0'] else options.grid +options.fill = 1 if options.blank and options.fill is None else options.fill + +# --- loop over input files ------------------------------------------------------------------------- if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) + if name is None and options.blank: + grid = np.array(list(map(int,options.grid))) + geom = damask.Geom(size=grid,microstructure=options.fill*np.ones(grid)) else: - geom = damask.Geom.from_file(name) - microstructure = geom.get_microstructure() - + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) + grid = geom.get_grid() - if options.grid is not None: - for i,g in enumerate(options.grid): - grid[i] = int(round(grid[i]*float(g.lower().replace('x','')))) if g.lower().endswith('x') \ - else int(options.grid[i]) + size = geom.get_size() + origin = geom.get_origin() + microstructure = geom.get_microstructure() + fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill + dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int - new = np.full(grid,options.fill if options.fill is not None else np.nanmax(microstructure)+1, - microstructure.dtype) + damask.util.croak(geom) - for x in range(microstructure.shape[0]): - X = x + options.offset[0] - if not 0 <= X < new.shape[0]: continue - for y in range(microstructure.shape[1]): - Y = y + options.offset[1] - if not 0 <= Y < new.shape[1]: continue - for z in range(microstructure.shape[2]): - Z = z + options.offset[2] - if not 0 <= Z < new.shape[2]: continue - new[X,Y,Z] = microstructure[x,y,z] +# --- do work ------------------------------------------------------------------------------------ + + new_grid = np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \ + else int(n) for o,n in zip(grid,options.grid)],dtype=int) + new_grid = np.where(new_grid > 0, new_grid,grid) - damask.util.croak(geom.update(new,rescale=True)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + microstructure_cropped = np.zeros(new_grid,dtype=dtype) + microstructure_cropped.fill(fill) + + if not options.blank: + xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+new_grid[0],grid[0])) + yindex = np.arange(max(options.offset[1],0),min(options.offset[1]+new_grid[1],grid[1])) + zindex = np.arange(max(options.offset[2],0),min(options.offset[2]+new_grid[2],grid[2])) + translate_x = [i - options.offset[0] for i in xindex] + translate_y = [i - options.offset[1] for i in yindex] + translate_z = [i - options.offset[2] for i in zindex] + if 0 in map(len,[xindex,yindex,zindex,translate_x,translate_y,translate_z]): + damask.util.croak('invaldid combination of grid and offset.') + continue + microstructure_cropped[min(translate_x):max(translate_x)+1, + min(translate_y):max(translate_y)+1, + min(translate_z):max(translate_z)+1] \ + = microstructure[min(xindex):max(xindex)+1, + min(yindex):max(yindex)+1, + min(zindex):max(zindex)+1] + + new_size = size/grid*new_grid if np.all(grid > 0) else new_grid + new_origin = origin + (size/grid if np.all(grid > 0) else new_size/new_grid) * options.offset + + geom.set_microstructure(microstructure_cropped) + geom.set_size(new_size) + geom.set_origin(new_origin) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_clean.py b/processing/pre/geom_clean.py index 66a205571..8fa7f5953 100755 --- a/processing/pre/geom_clean.py +++ b/processing/pre/geom_clean.py @@ -44,18 +44,14 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure() microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent, size=(options.stencil,)*3).astype(microstructure.dtype) damask.util.croak(geom.update(microstructure)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_fromMinimalSurface.py b/processing/pre/geom_fromMinimalSurface.py index d001b57d2..787b0628b 100755 --- a/processing/pre/geom_fromMinimalSurface.py +++ b/processing/pre/geom_fromMinimalSurface.py @@ -82,13 +82,14 @@ for name in filenames: Y = options.periods*2.0*np.pi*(np.arange(options.grid[1])+0.5)/options.grid[1] Z = options.periods*2.0*np.pi*(np.arange(options.grid[2])+0.5)/options.grid[2] - microstructure = np.empty(options.grid,dtype='int') + microstructure = np.empty(options.grid,dtype=int) for x in range(options.grid[0]): for y in range(options.grid[1]): for z in range(options.grid[2]): - microstructure[x,y,z]=options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])] + microstructure[x,y,z]=options.microstructure[int(options.threshold < surface[options.type](X[x],Y[y],Z[z]))] - geom=damask.Geom(microstructure,options.size,options.homogenization, + geom=damask.Geom(microstructure,options.size, + homogenization=options.homogenization, comments=[scriptID + ' ' + ' '.join(sys.argv[1:])]) damask.util.croak(geom) diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index 43bfe338e..b5d5c220c 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -171,7 +171,8 @@ for name in filenames: if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)] header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*origin)] - geom = damask.Geom(grain.reshape(grid,order='F'),size,options.homogenization,comments=header) + geom = damask.Geom(grain.reshape(grid,order='F'),size, + homogenization=options.homogenization,comments=header) damask.util.croak(geom) if name is None: diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index 1b0f5432f..46533fdc5 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -311,7 +311,8 @@ for name in filenames: config_header += [''] header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header + ['origin x {} y {} z {}'.format(*info['origin'])] - geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'],options.homogenization,comments=header) + geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'], + homogenization=options.homogenization,comments=header) damask.util.croak(geom) if name is None: diff --git a/processing/pre/geom_grainGrowth.py b/processing/pre/geom_grainGrowth.py index af044879e..952c15c13 100755 --- a/processing/pre/geom_grainGrowth.py +++ b/processing/pre/geom_grainGrowth.py @@ -59,11 +59,8 @@ options.immutable = list(map(int,options.immutable)) for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) + microstructure = geom.get_microstructure() damask.util.croak(geom) grid_original = geom.get_grid() @@ -171,7 +168,7 @@ for name in filenames: microstructure = np.where(immutable, microstructure_original,microstructure) damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_mirror.py b/processing/pre/geom_mirror.py index e2bf5f6dd..7933e416c 100755 --- a/processing/pre/geom_mirror.py +++ b/processing/pre/geom_mirror.py @@ -50,12 +50,8 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) - microstructure = geom.microstructure + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) + microstructure = geom.get_microstructure() if 'z' in options.directions: microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2) @@ -65,7 +61,7 @@ for name in filenames: microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0) damask.util.croak(geom.update(microstructure,rescale=True)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_pack.py b/processing/pre/geom_pack.py index 9816551b0..cc655c06d 100755 --- a/processing/pre/geom_pack.py +++ b/processing/pre/geom_pack.py @@ -29,14 +29,10 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) - damask.util.croak(geom) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure().flatten('F') - + damask.util.croak(geom) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) compressType = None former = start = -1 @@ -51,13 +47,13 @@ for name in filenames: reps += 1 else: if compressType is None: - out = [] + out = geom.get_header() elif compressType == '.': - out.append('{}\n'.format(former)) + out.append('{}'.format(former)) elif compressType == 'to': - out.append('{} to {}\n'.format(start,former)) + out.append('{} to {}'.format(start,former)) elif compressType == 'of': - out.append('{} of {}\n'.format(reps,former)) + out.append('{} of {}'.format(reps,former)) compressType = '.' start = current @@ -66,18 +62,18 @@ for name in filenames: former = current if compressType == '.': - out.append('{}\n'.format(former)) + out.append('{}'.format(former)) elif compressType == 'to': - out.append('{} to {}\n'.format(start,former)) + out.append('{} to {}'.format(start,former)) elif compressType == 'of': - out.append('{} of {}\n'.format(reps,former)) + out.append('{} of {}'.format(reps,former)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) - comments = geom.get_comments() - with open(name,'w') as f: - f.write('{} header\n'.format(3+len(comments))) - f.writelines(["{}\n".format(comment) for comment in comments]) - f.write('grid a {} b {} c {}\n'.format(*geom.get_grid())) - f.write('size x {} y {} z {}\n'.format(*geom.get_size())) - f.write('homogenization {}\n'.format(geom.get_homogenization())) - f.writelines(out) + + if name is None: + sys.stdout.write('\n'.join(out)+'\n') + else: + with open(name,'w') as f: + f.write('\n'.join(out)+'\n') + + + diff --git a/processing/pre/geom_renumber.py b/processing/pre/geom_renumber.py index 93c0ffebe..ef21cd1ab 100755 --- a/processing/pre/geom_renumber.py +++ b/processing/pre/geom_renumber.py @@ -31,11 +31,7 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure() renumbered = np.copy(microstructure) @@ -43,7 +39,7 @@ for name in filenames: renumbered = np.where(microstructure == oldID, i+1, renumbered) damask.util.croak(geom.update(renumbered)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py index 61f41f621..1a94f327e 100755 --- a/processing/pre/geom_rescale.py +++ b/processing/pre/geom_rescale.py @@ -2,9 +2,10 @@ import os import sys +import numpy as np + from io import StringIO from optparse import OptionParser - from scipy import ndimage import damask @@ -41,30 +42,25 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure() - - scale = geom.get_grid().astype('float') - if options.grid is not None: - for i,g in enumerate(options.grid): - scale[i] = scale[i]*float(g.lower().replace('x','')) if g.lower().endswith('x') \ - else float(options.grid[i])/scale[i] - + grid = geom.get_grid() size = geom.get_size() - if options.size is not None: - for i,s in enumerate(options.size): - size[i] = size[i]*float(s.lower().replace('x','')) if s.lower().endswith('x') \ - else options.size[i] - microstructure = ndimage.interpolation.zoom(microstructure, scale, output=microstructure.dtype, - order=0, mode='nearest', prefilter=False) + new_grid = grid if options.grid is None else \ + np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \ + else int(n) for o,n in zip(grid,options.grid)],dtype=int) - damask.util.croak(geom.update(microstructure,size)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + new_size = size if options.size is None else \ + np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \ + else float(n) for o,n in zip(size,options.size)],dtype=float) + + if np.any(new_grid != grid): + microstructure = ndimage.interpolation.zoom(microstructure, new_grid/grid,output=microstructure.dtype, + order=0,mode='nearest', prefilter=False) + + damask.util.croak(geom.update(microstructure,new_size)) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_rotate.py b/processing/pre/geom_rotate.py index 6a058f547..4189fefea 100755 --- a/processing/pre/geom_rotate.py +++ b/processing/pre/geom_rotate.py @@ -27,7 +27,7 @@ Rotates original microstructure and embeddeds it into buffer material. parser.add_option('-r', '--rotation', dest='rotation', type = 'float', nargs = 4, metavar = ' '.join(['float']*4), - help = 'rotation given as angle and axis') + help = 'rotation given as axis and angle') parser.add_option('-e', '--eulers', dest = 'eulers', type = 'float', nargs = 3, metavar = ' '.join(['float']*3), @@ -59,41 +59,38 @@ if [options.rotation,options.eulers,options.matrix,options.quaternion].count(Non parser.error('no rotation specified.') if options.quaternion is not None: - eulers = damask.Rotation.fromQuaternion(np.array(options.quaternion)).asEulers(degrees=True) + rot = damask.Rotation.fromQuaternion(np.array(options.quaternion)) # we might need P=+1 here, too... if options.rotation is not None: - eulers = damask.Rotation.fromAxisAngle(np.array(options.rotation,degrees=options.degrees)).asEulers(degrees=True) + rot = damask.Rotation.fromAxisAngle(np.array(options.rotation),degrees=options.degrees,P=+1) if options.matrix is not None: - eulers = damask.Rotation.fromMatrix(np.array(options.Matrix)).asEulers(degrees=True) + rot = damask.Rotation.fromMatrix(np.array(options.Matrix)) if options.eulers is not None: - eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees).asEulers(degrees=True) + rot = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees) +eulers = rot.asEulers(degrees=True) if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure() - - fill = options.fill if options.fill is not None else np.nanmax(microstructure)+1 - + fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill + dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int + # These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'') # this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0, - prefilter=False,output=microstructure.dtype,cval=fill) # rotation around z + prefilter=False,output=dtype,cval=fill) # rotation around z microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0, - prefilter=False,output=microstructure.dtype,cval=fill) # rotation around x + prefilter=False,output=dtype,cval=fill) # rotation around x microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0, - prefilter=False,output=microstructure.dtype,cval=fill) # rotation around z + prefilter=False,output=dtype,cval=fill) # rotation around z damask.util.croak(geom.update(microstructure,rescale=True)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_toTable.py b/processing/pre/geom_toTable.py index e21d081eb..352238524 100755 --- a/processing/pre/geom_toTable.py +++ b/processing/pre/geom_toTable.py @@ -31,20 +31,13 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) damask.util.croak(geom) microstructure = geom.get_microstructure().flatten('F') grid = geom.get_grid() size = geom.get_size() + origin = geom.get_origin() - for i,line in enumerate(geom.get_comments()): - if line.lower().strip().startswith('origin'): - origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z) - #--- generate grid -------------------------------------------------------------------------------- x = (0.5 + np.arange(grid[0],dtype=float))/grid[0]*size[0]+origin[0] @@ -58,7 +51,7 @@ for name in filenames: # ------------------------------------------ finalize output --------------------------------------- table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt' if name else name) - table.info_append([scriptID + '\t' + ' '.join(sys.argv[1:])] + geom.get_comments()) + table.info_append(geom.get_comments() + [scriptID + '\t' + ' '.join(sys.argv[1:])]) table.labels_append(['{}_{}'.format(1+i,'pos') for i in range(3)]+['microstructure']) table.head_write() table.output_flush() diff --git a/processing/pre/geom_translate.py b/processing/pre/geom_translate.py index 62cef3a2a..488da5103 100755 --- a/processing/pre/geom_translate.py +++ b/processing/pre/geom_translate.py @@ -43,36 +43,22 @@ parser.set_defaults(origin = (0.0,0.0,0.0), (options, filenames) = parser.parse_args() -sub = {} -for i in range(len(options.substitute)//2): # split substitution list into "from" -> "to" - sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1]) - +sub = list(map(int,options.substitute)) if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure() - new = np.copy(microstructure) + substituted = np.copy(microstructure) - for k, v in sub.items(): new[microstructure==k] = v # substitute microstructure indices and shift + for old,new in zip(sub[0::2],sub[1::2]): substituted[microstructure==old] = new # substitute microstructure indices + substituted += options.microstructure # constant shift - microstructure += options.microstructure # constant shift - - for i,line in enumerate(geom.get_comments()): - if line.lower().strip().startswith('origin'): - origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z) - origin += np.array(origin) - geom.comments[i] = 'origin x {} y {} z {}'.format(*origin) - - damask.util.croak(geom.update(microstructure)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin)) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_unpack.py b/processing/pre/geom_unpack.py index 028fc2e25..1c9b591be 100755 --- a/processing/pre/geom_unpack.py +++ b/processing/pre/geom_unpack.py @@ -29,14 +29,10 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) damask.util.croak(geom) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/processing/pre/geom_vicinityOffset.py b/processing/pre/geom_vicinityOffset.py index 49e419a65..e36aac301 100755 --- a/processing/pre/geom_vicinityOffset.py +++ b/processing/pre/geom_vicinityOffset.py @@ -41,10 +41,10 @@ parser.add_option('-v', '--vicinity', dest = 'vicinity', type = 'int', metavar = 'int', help = 'voxel distance checked for presence of other microstructure [%default]') -parser.add_option('-m', '--microstructureoffset', +parser.add_option('-o', '--offset', dest='offset', type = 'int', metavar = 'int', - help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index + 1') + help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index') parser.add_option('-t', '--trigger', dest = 'trigger', action = 'extend', metavar = '', @@ -69,14 +69,10 @@ if filenames == []: filenames = [None] for name in filenames: damask.util.report(scriptName,name) - if name is None: - virt_file = StringIO(''.join(sys.stdin.read())) - geom = damask.Geom.from_file(virt_file) - else: - geom = damask.Geom.from_file(name) + geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name) microstructure = geom.get_microstructure() - offset = options.offset if options.offset is not None else np.nanmax(microstructure) + offset = np.nanmax(microstructure) if options.offset is None else options.offset microstructure = np.where(ndimage.filters.generic_filter(microstructure, taintedNeighborhood, @@ -86,7 +82,7 @@ for name in filenames: microstructure + offset,microstructure) damask.util.croak(geom.update(microstructure)) - geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:])) + geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:])) if name is None: sys.stdout.write(str(geom.show())) diff --git a/python/damask/geom.py b/python/damask/geom.py index 46c378240..49dbacff8 100644 --- a/python/damask/geom.py +++ b/python/damask/geom.py @@ -9,110 +9,116 @@ from . import util class Geom(): """Geometry definition for grid solvers""" - def __init__(self,microstructure,size,homogenization=1,comments=[]): + def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]): """New geometry definition from array of microstructures and size""" - if len(microstructure.shape) != 3: - raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape)) - elif microstructure.dtype not in [int,float]: - raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype)) - else: - self.microstructure = microstructure + self.set_size(size) + self.set_origin(origin) + self.set_microstructure(microstructure) + self.set_homogenization(homogenization) + self.set_comments(comments) - if len(size) != 3 or any(np.array(size)<=0): - raise ValueError('Invalid size {}'.format(*size)) - else: - self.size = np.array(size) - - if not isinstance(homogenization,int) or homogenization < 1: - raise TypeError('Invalid homogenization {}'.format(homogenization)) - else: - self.homogenization = homogenization - - if not isinstance(comments,list): - self.comments = [str(comments)] - else: - self.comments = [str(comment) for comment in comments] def __repr__(self): """Basic information on geometry definition""" - return 'grid a b c: {}\n'.format(' x '.join(map(str,self.get_grid()))) + \ - 'size x y z: {}\n'.format(' x '.join(map(str,self.size))) + \ - 'homogenization: {}\n'.format(self.homogenization) + \ + return 'grid a b c: {}\n'.format(' x '.join(map(str,self.get_grid ()))) + \ + 'size x y z: {}\n'.format(' x '.join(map(str,self.get_size ()))) + \ + 'origin x y z: {}\n'.format(' x '.join(map(str,self.get_origin()))) + \ + 'homogenization: {}\n'.format(self.get_homogenization()) + \ '# microstructures: {}\n'.format(len(np.unique(self.microstructure))) + \ - 'max microstructures: {}\n'.format(np.max(self.microstructure)) + 'max microstructures: {}\n'.format(np.nanmax(self.microstructure)) - def update(self,microstructure=None,size=None,rescale=False): + def update(self,microstructure=None,size=None,origin=None,rescale=False): """Updates microstructure and size""" grid_old = self.get_grid() size_old = self.get_size() + origin_old = self.get_origin() unique_old = len(np.unique(self.microstructure)) - max_old = np.max(self.microstructure) + max_old = np.nanmax(self.microstructure) if size is not None and rescale: raise ValueError('Either set size explicitly or rescale automatically') + self.set_microstructure(microstructure) + self.set_size(self.get_grid()/grid_old if rescale else size) + self.set_origin(origin) + + message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))] + if np.any(grid_old != self.get_grid()): + message[-1] = util.delete(message[-1]) + message.append('grid a b c: {}'.format(' x '.join(map(str,self.get_grid())))) + + message.append('size x y z: {}'.format(' x '.join(map(str,size_old)))) + if np.any(size_old != self.get_size()): + message[-1] = util.delete(message[-1]) + message.append('size x y z: {}'.format(' x '.join(map(str,self.get_size())))) + + message.append('origin x y z: {}'.format(' x '.join(map(str,origin_old)))) + if np.any(origin_old != self.get_origin()): + message[-1] = util.delete(message[-1]) + message.append('origin x y z: {}'.format(' x '.join(map(str,self.get_origin())))) + + message.append('homogenization: {}'.format(self.get_homogenization())) + + message.append('# microstructures: {}'.format(unique_old)) + if unique_old != len(np.unique(self.microstructure)): + message[-1] = util.delete(message[-1]) + message.append('# microstructures: {}'.format(len(np.unique(self.microstructure)))) + + message.append('max microstructure: {}'.format(max_old)) + if max_old != np.nanmax(self.microstructure): + message[-1] = util.delete(message[-1]) + message.append('max microstructure: {}'.format(np.nanmax(self.microstructure))) + + return util.srepr(message) + + def set_comments(self,comments): + self.comments = [] + self.add_comments(comments) + + def add_comments(self,comments): + self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)] + + def set_microstructure(self,microstructure): if microstructure is not None: if len(microstructure.shape) != 3: raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape)) - elif microstructure.dtype not in ['int','float']: + elif microstructure.dtype not in [int,float]: raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype)) else: - self.microstructure = microstructure - + self.microstructure = np.copy(microstructure) + + def set_size(self,size): if size is not None: if len(size) != 3 or any(np.array(size)<=0): raise ValueError('Invalid size {}'.format(*size)) else: self.size = np.array(size) - - if rescale: - self.size = self.size * self.get_grid()/grid_old - - message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))] - if np.any(grid_old != self.get_grid()): - message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC - message.append('grid a b c: {}'.format(' x '.join(map(str,self.get_grid())))) - message.append('size x y z: {}'.format(' x '.join(map(str,size_old)))) - if np.any(size_old != self.size): - message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC - message.append('size x y z: {}'.format(' x '.join(map(str,self.size)))) + def set_origin(self,origin): + if origin is not None: + if len(origin) != 3: + raise ValueError('Invalid origin {}'.format(*origin)) + else: + self.origin = np.array(origin) - message.append('homogenization: {}'.format(self.homogenization)) - - message.append('# microstructures: {}'.format(unique_old)) - if unique_old != len(np.unique(self.microstructure)): - message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC - message.append('# microstructures: {}'.format(len(np.unique(self.microstructure)))) - - message.append('max microstructures: {}'.format(max_old)) - if max_old != np.max(self.microstructure): - message[-1] = util.bcolors.CROSSOUT+message[-1]+util.bcolors.ENDC - message.append('max microstructures: {}'.format(np.max(self.microstructure))) - - return '\n'.join(message) + def set_homogenization(self,homogenization): + if homogenization is not None: + if not isinstance(homogenization,int) or homogenization < 1: + raise TypeError('Invalid homogenization {}'.format(homogenization)) + else: + self.homogenization = homogenization - def add_comment(self,comment): - if not isinstance(comment,list): - self.comments = [str(comment)] + self.comments - else: - self.comments = [str(c) for c in comment] + self.comments - - def set_microstructure(self,microstructure): - self.microstructure = np.copy(microstructure) - - def set_size(self,size): - self.size = np.array(size) - - def get_microstructure(self): return np.copy(self.microstructure) def get_size(self): return np.copy(self.size) + def get_origin(self): + return np.copy(self.origin) + def get_grid(self): return np.array(self.microstructure.shape) @@ -122,42 +128,44 @@ class Geom(): def get_comments(self): return self.comments[:] + def get_header(self): + header = ['{} header'.format(len(self.comments)+4)] + self.comments + header.append('grid a {} b {} c {}'.format(*self.get_grid())) + header.append('size x {} y {} z {}'.format(*self.get_size())) + header.append('origin x {} y {} z {}'.format(*self.get_origin())) + header.append('homogenization {}'.format(self.get_homogenization())) + return header + @classmethod def from_file(cls,fname): - """Reads from *.geom file""" - if isinstance(fname,str): - f = open(fname) - header_length,keyword = f.readline().split() - if not keyword.startswith('head') or int(header_length) < 3: - raise TypeError('Header length information missing or invalid') - comments_old = [f.readline() for i in range(int(header_length))] - else: - fname.seek(0) - header_length,keyword = fname.readline().split() - if not keyword.startswith('head') or int(header_length) < 3: - raise TypeError('Header length information missing or invalid') - comments_old = [fname.readline() for i in range(int(header_length))] + """Reads a geom file""" + with (open(fname) if isinstance(fname,str) else fname) as f: + f.seek(0) + header_length,keyword = f.readline().split()[:2] + header_length = int(header_length) + content = f.readlines() + + if not keyword.startswith('head') or header_length < 3: + raise TypeError('Header length information missing or invalid') comments = [] - for i,line in enumerate(comments_old): - if line.lower().strip().startswith('grid'): - grid = np.array([int(line.split()[j]) for j in [2,4,6]]) # assume correct order (a,b,c) - elif line.lower().strip().startswith('size'): - size = np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z) - elif line.lower().strip().startswith('homogenization'): - homogenization = int(line.split()[1]) + for i,line in enumerate(content[:header_length]): + items = line.lower().strip().split() + key = items[0] if len(items) > 0 else '' + if key == 'grid': + grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']]) + elif key == 'size': + size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']]) + elif key == 'origin': + origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']]) + elif key == 'homogenization': + homogenization = int(items[1]) else: - comments.append(line.rstrip().strip()) - - if isinstance(fname,str): - raw = f.readlines() - f.close() - else: - raw = fname.readlines() + comments.append(line.strip()) microstructure = np.empty(grid.prod()) # initialize as flat array i = 0 - for line in raw: + for line in content[header_length:]: items = line.split() if len(items) == 3: if items[1].lower() == 'of': @@ -175,28 +183,19 @@ class Geom(): raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i)) microstructure = microstructure.reshape(grid,order='F') - - if '.' in raw[0]: # contains float values - pass - else: # assume int values + if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present microstructure = microstructure.astype('int') - return cls(microstructure.reshape(grid),size,homogenization,comments) + return cls(microstructure.reshape(grid),size,origin,homogenization,comments) def to_file(self,fname): - """Saves to file""" - grid = self.get_grid() - header = ['{} header'.format(len(self.comments)+3)] - header += self.comments - header.append('grid a {} b {} c {}'.format(*grid)) - header.append('size x {} y {} z {}'.format(*self.size)) - header.append('homogenization {}'.format(self.get_homogenization())) - - if self.microstructure.dtype == 'int': - format_string='%{}i'.format(int(math.floor(math.log10(self.microstructure.max())+1))) - else: - format_string='%.18e' - np.savetxt(fname, self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T, + """Writes to file""" + header = self.get_header() + grid = self.get_grid() + format_string = '%{}i'.format(int(math.floor(math.log10(self.microstructure.max())+1))) if self.microstructure.dtype == int \ + else '%g' + np.savetxt(fname, + self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T, header='\n'.join(header), fmt=format_string, comments='') def show(self): diff --git a/python/damask/util.py b/python/damask/util.py index 7f0f3ab56..d11b74a7b 100644 --- a/python/damask/util.py +++ b/python/damask/util.py @@ -85,6 +85,11 @@ def delete(what): """Dims string""" return bcolors.DIM+srepr(what)+bcolors.ENDC +# ----------------------------- +def strikeout(what): + """Dims string""" + return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC + # ----------------------------- def execute(cmd, streamIn = None, diff --git a/test.log b/test.log new file mode 100644 index 000000000..a9dbb8c45 --- /dev/null +++ b/test.log @@ -0,0 +1,211 @@ +2019-05-27 22:44:00,700 - INFO: +++++++++++++++++++++++++++++++++++++++++ +---------------------------------------- +| Check geom-modifying scripts +---------------------------------------- +2019-05-27 22:44:00,707 - INFO: +geom_addPrimitive -c 0.3 0.5 0.2 -a 1.0 0.8 0.9 0.4 -d 0.10 0.13 0.08 geom_addPrimitive.geom +2019-05-27 22:44:00,899 - INFO: +geom_addPrimitive: geom_addPrimitive.geom + +grid a b c: 32 x 35 x 12 +size x y z: 0.914285714286 x 1.0 x 0.342857142857 +origin x y z: 0.0 x 1.0 x 2.0 +homogenization: 1 +# microstructures: 20 +max microstructure: 26 + +2019-05-27 22:44:00,899 - DEBUG: + +2019-05-27 22:44:00,899 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_addPrimitive_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_addPrimitive.geom +2019-05-27 22:44:00,920 - INFO: +geom_canvas -g 40 35 20 -f 90 geom_canvas.geom +2019-05-27 22:44:01,103 - INFO: +geom_canvas: geom_canvas.geom + +grid a b c: 32 x 35 x 12 +size x y z: 0.914285714286 x 1.0 x 0.342857142857 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 20 +max microstructures: 20 + + +2019-05-27 22:44:01,103 - DEBUG: + +2019-05-27 22:44:01,104 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_canvas_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_canvas.geom +2019-05-27 22:44:01,135 - INFO: +geom_clean -s 2 geom_clean.geom +2019-05-27 22:44:03,219 - INFO: +geom_clean: geom_clean.geom + +grid a b c: 53 x 52 x 52 +size x y z: 1.0 x 0.981132075472 x 0.981132075472 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 23 +max microstructure: 23 + +2019-05-27 22:44:03,219 - DEBUG: + +2019-05-27 22:44:03,219 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_clean_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_clean.geom +2019-05-27 22:44:03,378 - INFO: +geom_grainGrowth -N2 -i 4 -d 2 geom_grainGrowth.geom +2019-05-27 22:44:04,065 - INFO: +geom_grainGrowth: geom_grainGrowth.geom + +grid a b c: 40 x 40 x 40 +size x y z: 1.0 x 1.0 x 1.0 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 15 +max microstructures: 15 + +grid a b c: 40 x 40 x 40 +size x y z: 1.0 x 1.0 x 1.0 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 15 +max microstructure: 15 + +2019-05-27 22:44:04,065 - DEBUG: + +2019-05-27 22:44:04,065 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_grainGrowth_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_grainGrowth.geom +2019-05-27 22:44:04,131 - INFO: +geom_mirror -d x,y,z --double geom_mirror.geom +2019-05-27 22:44:04,330 - INFO: +geom_mirror: geom_mirror.geom + +grid a b c: 32 x 35 x 12 +grid a b c: 64 x 70 x 24 +size x y z: 0.914285714286 x 1.0 x 0.342857142857 +size x y z: 2.0 x 2.0 x 2.0 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 20 +max microstructure: 20 + +2019-05-27 22:44:04,331 - DEBUG: + +2019-05-27 22:44:04,331 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_mirror_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_mirror.geom +2019-05-27 22:44:04,447 - INFO: +geom_renumber geom_renumber.geom +2019-05-27 22:44:04,688 - INFO: +geom_renumber: geom_renumber.geom + +grid a b c: 53 x 52 x 52 +size x y z: 1.0 x 0.981132075472 x 0.981132075472 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 23 +max microstructure: 42 +max microstructure: 23 + +2019-05-27 22:44:04,688 - DEBUG: + +2019-05-27 22:44:04,688 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_renumber_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_renumber.geom +2019-05-27 22:44:04,864 - INFO: +geom_rescale -g 20 22 20 -s 0.1 0.2 0.3 geom_rescale.geom +2019-05-27 22:44:05,109 - INFO: +geom_rescale: geom_rescale.geom + +grid a b c: 32 x 35 x 12 +grid a b c: 20 x 22 x 20 +size x y z: 0.914285714286 x 1.0 x 0.342857142857 +size x y z: 0.1 x 0.2 x 0.3 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 20 +max microstructure: 20 + +2019-05-27 22:44:05,109 - DEBUG: + +2019-05-27 22:44:05,109 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_rescale_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_rescale.geom +2019-05-27 22:44:05,122 - INFO: +geom_rotate -d -e 45 45 0 geom_rotate.geom +2019-05-27 22:44:05,529 - INFO: +geom_rotate: geom_rotate.geom + +grid a b c: 53 x 52 x 52 +grid a b c: 90 x 90 x 74 +size x y z: 1.0 x 0.981132075472 x 0.981132075472 +size x y z: 1.6981132075471699 x 1.7307692307692308 x 1.4230769230769231 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 23 +# microstructures: 24 +max microstructure: 23 +max microstructure: 24 + +2019-05-27 22:44:05,530 - DEBUG: + +2019-05-27 22:44:05,530 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_rotate_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_rotate.geom +2019-05-27 22:44:06,282 - INFO: +geom_translate -o 0 1 2 -m 6 geom_translate.geom +2019-05-27 22:44:06,469 - INFO: +geom_translate: geom_translate.geom + +grid a b c: 32 x 35 x 12 +size x y z: 0.914285714286 x 1.0 x 0.342857142857 +origin x y z: 0.0 x 0.0 x 0.0 +origin x y z: 0.0 x 1.0 x 2.0 +homogenization: 1 +# microstructures: 20 +max microstructure: 20 +max microstructure: 26 + +2019-05-27 22:44:06,469 - DEBUG: + +2019-05-27 22:44:06,469 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_translate_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_translate.geom +2019-05-27 22:44:06,486 - INFO: +geom_vicinityOffset -v 2 geom_vicinityOffset.geom +2019-05-27 22:44:07,005 - INFO: +geom_vicinityOffset: geom_vicinityOffset.geom + +grid a b c: 40 x 40 x 40 +size x y z: 1.0 x 1.0 x 1.0 +origin x y z: 0.0 x 0.0 x 0.0 +homogenization: 1 +# microstructures: 5 +# microstructures: 10 +max microstructure: 5 +max microstructure: 10 + +2019-05-27 22:44:07,005 - DEBUG: + +2019-05-27 22:44:07,005 - INFO: +comparing + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/reference/geom_vicinityOffset_reference.geom + /Users/philip/Documents/DAMASK/PRIVATE/testing/PreProcessing_GeomModification/current/geom_vicinityOffset.geom +2019-05-27 22:44:07,076 - CRITICAL: +**************************************** +All 10 tests passed. +**************************************** +